From 1e3fd1bef2a0ec1c8b73fcfefdd62fd3463bc87c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 27 Nov 2020 18:35:56 +0100 Subject: Improved way to have persistent DLLs for mkinmod Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package. --- R/mkinmod.R | 60 +++++++++++++++++++++++++++++++++++------------------------- 1 file changed, 35 insertions(+), 25 deletions(-) (limited to 'R/mkinmod.R') diff --git a/R/mkinmod.R b/R/mkinmod.R index 434282fd..a7353e81 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -11,6 +11,7 @@ #' of the system of differential equations is included in the resulting #' mkinmod object in some cases, speeding up the solution. #' +#' If a C compiler is found by [pkgbuild::has_compiler()] and there #' is more than one observed variable in the specification, C code is generated #' for evaluating the differential equations, compiled using #' [inline::cfunction()] and added to the resulting mkinmod object. @@ -34,15 +35,21 @@ #' formation fractions are always used (default). If "min", a minimum use of #' formation fractions is made, i.e. each pathway to a metabolite has its #' own rate constant. -#' @param name A name for the model. Should be a valid R object name. #' @param speclist The specification of the observed variables and their #' submodel types and pathways can be given as a single list using this #' argument. Default is NULL. #' @param quiet Should messages be suppressed? #' @param verbose If \code{TRUE}, passed to [inline::cfunction()] if #' applicable to give detailed information about the C function being built. -#' @param cf_dir Directory where CFunc objects should be saved. Specifying -#' 'cf_dir' without specifying a 'name' for the object is an error. +#' @param name A name for the model. Should be a valid R object name. +#' @param dll_dir Directory where an DLL object, if generated internally by +#' [inline::cfunction()], should be saved. The DLL will only be stored in a +#' permanent location for use in future sessions, if 'dll_dir' and 'name' +#' are specified. +#' @param unload If a DLL from the target location in 'dll_dir' is already +#' loaded, should that be unloaded first? +#' @param overwrite If a file exists at the target DLL location in 'dll_dir', +#' should this be overwritten? #' @importFrom methods signature #' @return A list of class \code{mkinmod} for use with [mkinfit()], #' containing, among others, @@ -95,12 +102,20 @@ #' \dontrun{ #' fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") #' -#' # Now supplying full names used for plotting, and write to user defined location +#' # Now supplying compound names used for plotting, and write to user defined location +#' # We need to choose a path outside the session tempdir because this gets removed +#' DLL_dir <- "~/.local/share/mkin" +#' if (!dir.exists(DLL_dir)) dir.create(DLL_dir) #' SFO_SFO.2 <- mkinmod( #' parent = mkinsub("SFO", "m1", full_name = "Test compound"), #' m1 = mkinsub("SFO", full_name = "Metabolite M1"), -#' name = "SFOSFO", cf_dir = tempdir()) -#' fit_sfo_sfo <- mkinfit(SFO_SFO.2, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +#' name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) +#' # Now we can save the model and restore it in a new session +#' saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") +#' # Terminate the R session here if you would like to check, and then do +#' library(mkin) +#' SFO_SFO.3 <- readRDS("~/SFO_SFO.rds") +#' fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") #' #' # Show details of creating the C function #' SFO_SFO <- mkinmod( @@ -126,15 +141,17 @@ #' #' @export mkinmod mkinmod <- function(..., use_of_ff = "max", name = NULL, - speclist = NULL, quiet = FALSE, verbose = FALSE, cf_dir = NULL) + speclist = NULL, quiet = FALSE, verbose = FALSE, dll_dir = NULL, + unload = FALSE, overwrite = FALSE) { if (is.null(speclist)) spec <- list(...) else spec <- speclist obs_vars <- names(spec) - if (!is.null(cf_dir)) { - if (!dir.exists(cf_dir)) stop(cf_dir, " does not exist") - if (is.null(name)) stop("You must give a name if you want to use 'cf_dir'") + save_msg <- "You need to specify both 'name' and 'dll_dir' to save a model DLL" + if (!is.null(dll_dir)) { + if (!dir.exists(dll_dir)) stop(dll_dir, " does not exist") + if (is.null(name)) stop(save_msg) } # Check if any of the names of the observed variables contains any other @@ -310,7 +327,7 @@ mkinmod <- function(..., use_of_ff = "max", name = NULL, } #}}} } #}}} - model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff) + model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff, name = name) # Create coefficient matrix if possible #{{{ if (mat) { @@ -438,26 +455,19 @@ mkinmod <- function(..., use_of_ff = "max", name = NULL, "}\n\n") # Try to build a shared library - cf <- try(inline::cfunction(derivs_sig, derivs_code, + model$cf <- try(inline::cfunction(derivs_sig, derivs_code, otherdefs = initpar_code, - verbose = verbose, + verbose = verbose, name = "diffs", convention = ".C", language = "C"), silent = TRUE) - if (!inherits(cf, "try-error")) { - if (is.null(cf_dir)) { - model$cf <- cf + if (!inherits(model$cf, "try-error")) { + if (is.null(dll_dir)) { if (!quiet) message("Temporary DLL for differentials generated and loaded") + dll_info <- inline::getDynLib(model$cf) } else { - cf_file <- inline::writeDynLib(cf, name, cf_dir) - model$cf <- inline::readDynLib(name, cf_dir) - model$cf_name <- name - model$cf_dir <- cf_dir - fileDLL <- inline::getDynLib(model$cf)[["path"]] - if (!quiet) { - message("CFunc object written to ", cf_file) - message("DLL written to ", fileDLL) - } + dll_info <- inline::moveDLL(model$cf, name, dll_dir, + unload = unload, overwrite = overwrite, verbose = !quiet) } } } -- cgit v1.2.1